Whole Genome Analysis of Selected Human Group A Rotavirus Strains Revealed Evolution of DS-1-Like Single- and Double-Gene Reassortant Rotavirus Strains in Pakistan During 2015–2016

Figures

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  FIGURE 1. Comparison of the genotype constellation of 5 Pakistani strains (PAK56, PAK622, PAK585, PAK419 and PAK663) having the G9P[8], G3P[8], G1P[8], G3P[4], and G3P[4] genotypes, respectively, compared with those of selected human and animal strains. The green and red shading represent human Wa-like, and DS-1-like genotypes, respectively. Different shades of green are used for VP7 G genotypes mostly found in combination with the Wa-like genotype constellation. Yellow is used to indicate gene segments of bovine origin and purple gene segments of caprine origin.

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  FIGURE 2. Phylogenetic tree constructed from the nucleotide sequences of the VP7 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 3. Phylogenetic tree constructed from the nucleotide sequences of the VP4 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.1 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 4. Phylogenetic tree constructed from the nucleotide sequences of the NSP2 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.02 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 5. Phylogenetic tree constructed from the nucleotide sequences of the NSP3 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 6. Phylogenetic tree constructed from the nucleotide sequences of the VP1 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 7. Phylogenetic tree constructed from the nucleotide sequences of the VP3 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 8. Phylogenetic tree constructed from the nucleotide sequences of the VP6 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.1 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 9. Phylogenetic tree constructed from the nucleotide sequences of the NSP1 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.1 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 10. Phylogenetic tree constructed from the nucleotide sequences of the NSP4 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.5 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 11. Phylogenetic tree constructed from the nucleotide sequences of the NSP5 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.

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  FIGURE 12. Phylogenetic tree constructed from the nucleotide sequences of the VP2 genes of the study strains and representative RVA strains. RVA strains sequenced in this study are represented by the red color. The vaccine strains and an out group strain are represented by Blue and green color, respectively while black shading represent strains isolated all over the world. The RVA strains sequenced in this study and reference strains obtained from GenBank database are represented by Accession number, Strain Name, Country and year of Isolation. Scale bar: 0.05 substitutions per nucleotide. Bootstrap values <60 are not shown.